1 Overview

Data

Normalization

Model options

Network processing

cor/cov method: pearson

2 Load and normalize data

Data

Normalization

2.1 Load TCGA data

See prepare.tcga.survival.data function for how to configure parameters.

This uses data packages from obtained from ‘github:averissimo/tcga’ that contain FPKM expression levels.

prepare.tcga.survival.data('kirc.data.2018.10.17',
                           'primary.solid.tumor',
                            normalization        = 'center',
                            log2.pre.normalize   = TRUE,
                            handle.duplicates    = 'keep_first',
                            coding.genes         = TRUE,
                            subtract.surv.column = '')

2.1.1 Summary of data

## [INFO]        Loaded data from TCGA: kirc.data.2018.10.17
## [INFO]               type of tissue: primary.solid.tumor
## [INFO]   observations (individuals): 463 (151 event / 312 censored)
## [INFO]            variables (genes): 19867

2.1.2 Survival curve

2.2 Load degree data

Network processing

  • Degree calculation: string
  • Edge cutoff: 0
  • Unweighted edges

cor/cov method: pearson

  • only applies if network type is correlation/covariance

2.3 Preparing degree vector

  • Normalize degree between 0 and 1
  • Hub: heuristic( 1 - degree )
  • Orphan: heuristic( degree )
  • trans.fun is a double power to scale the values

see ?glmSparseNet::heuristicScale or ?glmSparseNet::hubHeuristic

# see ?glmSparseNet::heuristic.scale
trans.fun <- function(x) {
    heuristicScale(x) + 0.2
}

2.3.1 Genes with degree above 4000

ensembl_gene_id degree external_gene_name
ENSG00000150991 10394 UBC
ENSG00000170325 6346 PRDM10
ENSG00000100300 5797 TSPO
ENSG00000174775 5614 HRAS
ENSG00000142208 5573 AKT1
ENSG00000111640 5363 GAPDH
ENSG00000163631 5260 ALB
ENSG00000177606 4952 JUN
ENSG00000141510 4936 TP53
ENSG00000197122 4903 SRC
ENSG00000254647 4592 INS
ENSG00000112062 4187 MAPK14
ENSG00000170315 4114 UBB
ENSG00000170345 4010 FOS

2.3.2 Original degree frequency

Original

LOG10 Scale on X-axis

3 Model Inference

3.1 Train and test sets

## [INFO] Size of sets: (size/events)
##  * Train: 80.00% ::  369 /  120
##  *  Test: 20.00% ::   94 /  31
## [INFO] Number of variables per model:
Model BaseModel Alpha TargetVars nvars
Elastic Net Elastic Net 0.20 69 69
Hub Elastic Net 0.20 69 69
Orphan Elastic Net 0.20 69 71
Elastic Net Hub 0.10 41 42
Hub Hub 0.10 41 43
Orphan Hub 0.10 41 44
Elastic Net Orphan 0.10 38 42
Hub Orphan 0.10 38 38
Orphan Orphan 0.10 38 39 
## [INFO] note, selected variables could be slightly different from target, to have more accuracy increase nlambda in code

4 Results

4.1 Relative risk distribution

Calculated using the inferred models and the train/test datasets. The higher the better.

Test Set

Train Set

4.2 Kaplan-Meier Curves

4.2.1 Models on test sets

Elastic Net (base model: Elastic Net)

Test set

Training set

Hub (base model: Elastic Net)

Test set

Training set

Orphan (base model: Elastic Net)

Test set

Training set

Elastic Net (base model: Hub)

Test set

Training set

Hub (base model: Hub)

Test set

Training set

Orphan (base model: Hub)

Test set

Training set

Elastic Net (base model: Orphan)

Test set

Training set

Hub (base model: Orphan)

Test set

Training set

Orphan (base model: Orphan)

Test set

Training set

4.3 Summary Table

weighted penalization project tissue cutoff coding.genes alpha model nvars km.train km.test c.index.train c.index.test
FALSE string kirc.data.2018.10.17 primary.solid.tumor 0 TRUE 0.20 Elastic Net 69 0 0.4800231 0.7989845 0.6002055
FALSE string kirc.data.2018.10.17 primary.solid.tumor 0 TRUE 0.20 Hub 69 0 0.4312017 0.7874588 0.6264132
FALSE string kirc.data.2018.10.17 primary.solid.tumor 0 TRUE 0.20 Orphan 71 0 0.3280982 0.7811956 0.5837616
FALSE string kirc.data.2018.10.17 primary.solid.tumor 0 TRUE 0.10 Elastic Net 42 0 0.3995605 0.7425416 0.6192189
FALSE string kirc.data.2018.10.17 primary.solid.tumor 0 TRUE 0.10 Hub 43 0 0.3531275 0.7465812 0.5858171
FALSE string kirc.data.2018.10.17 primary.solid.tumor 0 TRUE 0.10 Orphan 44 0 0.6813939 0.7269392 0.5904419
FALSE string kirc.data.2018.10.17 primary.solid.tumor 0 TRUE 0.10 Elastic Net 42 0 0.3995605 0.7425416 0.6192189
FALSE string kirc.data.2018.10.17 primary.solid.tumor 0 TRUE 0.10 Hub 38 0 0.4517998 0.7417633 0.5781089
FALSE string kirc.data.2018.10.17 primary.solid.tumor 0 TRUE 0.10 Orphan 39 0 0.9453068 0.7252715 0.5919836

4.4 Non-zero genes

4.4.1 Venn Diagram of selected genes

4.4.1.1 Overlap between models (with same target number of variables)

Base model: Elastic Net with Target Vars: 69 and Alpha: 0.20

Base model: Hub with Target Vars: 41 and Alpha: 0.10

Base model: Orphan with Target Vars: 38 and Alpha: 0.10

Table of genes in models

(not running at the moment)

5 5000 Runs

5.1 C-Index distribution

Test set

Summary of C-Index and Log-rank

metric model base.model target.vars alpha mean std median min
C-Index (Test set) Hub Elastic Net 69 0.20 0.666 0.047 0.667 0.455
C-Index (Test set) Hub Hub 41 0.10 0.661 0.048 0.662 0.426
C-Index (Test set) Hub Orphan 38 0.10 0.660 0.048 0.661 0.427
C-Index (Test set) Elastic Net Elastic Net 69 0.20 0.687 0.045 0.688 0.501
C-Index (Test set) Elastic Net Hub 41 0.10 0.669 0.050 0.670 0.481
C-Index (Test set) Elastic Net Orphan 38 0.10 0.668 0.050 0.669 0.481
C-Index (Test set) Orphan Elastic Net 69 0.20 0.672 0.046 0.673 0.481
C-Index (Test set) Orphan Hub 41 0.10 0.659 0.050 0.661 0.45
C-Index (Test set) Orphan Orphan 38 0.10 0.658 0.051 0.659 0.445
Log-rank (Test set) Hub Elastic Net 69 0.20 0.044 0.103 0.007 2.57e-09
Log-rank (Test set) Hub Hub 41 0.10 0.061 0.122 0.013 4.23e-09
Log-rank (Test set) Hub Orphan 38 0.10 0.065 0.127 0.015 1.16e-08
Log-rank (Test set) Elastic Net Elastic Net 69 0.20 0.030 0.081 0.004 2.51e-09
Log-rank (Test set) Elastic Net Hub 41 0.10 0.059 0.127 0.011 1.36e-10
Log-rank (Test set) Elastic Net Orphan 38 0.10 0.060 0.128 0.012 1.36e-10
Log-rank (Test set) Orphan Elastic Net 69 0.20 0.046 0.103 0.008 5.88e-12
Log-rank (Test set) Orphan Hub 41 0.10 0.075 0.144 0.017 5.92e-09
Log-rank (Test set) Orphan Orphan 38 0.10 0.077 0.147 0.017 5.92e-09

C-Index Distribution

Rank

Elastic Net vs Hub
base.model r.squared
Elastic Net with target nvars: 69 alpha: 0.20 0.6464047
Hub with target nvars: 41 alpha: 0.10 0.6503503
Orphan with target nvars: 38 alpha: 0.10 0.6376429

Elastic Net vs. Orphan
base.model r.squared
Elastic Net with target nvars: 69 alpha: 0.20 0.9177439
Hub with target nvars: 41 alpha: 0.10 0.9428788
Orphan with target nvars: 38 alpha: 0.10 0.9409778

Hub vs. Orphan
base.model r.squared
Elastic Net with target nvars: 69 alpha: 0.20 0.6248941
Hub with target nvars: 41 alpha: 0.10 0.6130614
Orphan with target nvars: 38 alpha: 0.10 0.5999652

Train set

Summary of C-Index and Log-rank

metric model base.model target.vars alpha mean std median min
C-Index (Train set) Hub Elastic Net 69 0.20 0.778 0.011 0.778 0.735
C-Index (Train set) Hub Hub 41 0.10 0.725 0.011 0.725 0.685
C-Index (Train set) Hub Orphan 38 0.10 0.721 0.011 0.721 0.683
C-Index (Train set) Elastic Net Elastic Net 69 0.20 0.780 0.011 0.780 0.74
C-Index (Train set) Elastic Net Hub 41 0.10 0.726 0.012 0.726 0.685
C-Index (Train set) Elastic Net Orphan 38 0.10 0.724 0.012 0.724 0.683
C-Index (Train set) Orphan Elastic Net 69 0.20 0.772 0.011 0.773 0.738
C-Index (Train set) Orphan Hub 41 0.10 0.717 0.011 0.717 0.673
C-Index (Train set) Orphan Orphan 38 0.10 0.715 0.012 0.715 0.67
Log-rank (Train set) Hub Elastic Net 69 0.20 0.000 0.000 0.000 0
Log-rank (Train set) Hub Hub 41 0.10 0.000 0.000 0.000 0
Log-rank (Train set) Hub Orphan 38 0.10 0.000 0.000 0.000 0
Log-rank (Train set) Elastic Net Elastic Net 69 0.20 0.000 0.000 0.000 0
Log-rank (Train set) Elastic Net Hub 41 0.10 0.000 0.000 0.000 0
Log-rank (Train set) Elastic Net Orphan 38 0.10 0.000 0.000 0.000 0
Log-rank (Train set) Orphan Elastic Net 69 0.20 0.000 0.000 0.000 0
Log-rank (Train set) Orphan Hub 41 0.10 0.000 0.000 0.000 0
Log-rank (Train set) Orphan Orphan 38 0.10 0.000 0.000 0.000 0

C-Index Distribution

C-Index Rank

5.2 Log-rank test on Kaplan-Meier models

5.2.1 Log-Rank distribution

Cumulative

Distribution of Log-rank test with groups separated by high and low risk groups

Distribution

Distribution of Log-rank test with groups separated by high and low risk groups

5.2.2 Log-Rank Rank

5.2.2.1 Elastic Net vs Hub

base.model r.squared
Elastic Net with target nvars: 69 alpha: 0.20 0.1939069
Hub with target nvars: 41 alpha: 0.10 0.2725566
Orphan with target nvars: 38 alpha: 0.10 0.2697257

5.2.2.2 Elastic Net vs. Orphan

base.model r.squared
Elastic Net with target nvars: 69 alpha: 0.20 0.4891016
Hub with target nvars: 41 alpha: 0.10 0.6118420
Orphan with target nvars: 38 alpha: 0.10 0.6275918

5.2.2.3 Hub vs. Orphan

base.model r.squared
Elastic Net with target nvars: 69 alpha: 0.20 0.2155423
Hub with target nvars: 41 alpha: 0.10 0.2623372
Orphan with target nvars: 38 alpha: 0.10 0.2646656

5.3 Consesus genes

5.3.1 Selected genes over all runs

Bar plots of frequencies

Overlap between variables selected

Base model: Elastic Net with Target Vars: 69 and Alpha: 0.20

Base model: Hub with Target Vars: 41 and Alpha: 0.10

Base model: Orphan with Target Vars: 38 and Alpha: 0.10

5.3.2 Selected genes in significant runs

i.e. with pvalue < 0.05 in Log-rank test using the test set.

Bar plots of frequencies

Overlap between variables selected

5.3.2.0.1 Base model Elastic Net with target nvars: 0.20 alpha: 69

5.3.2.0.2 Base model Hub with target nvars: 0.10 alpha: 41

5.3.2.0.3 Base model Orphan with target nvars: 0.10 alpha: 38

5.3.3 Genes in Significant runs

i.e. with pvalue < 0.05 in Log-rank test using the test set.

Top consensus 20 genes

Gene Overlap total
ADM5 2 22238
AR 2 21690
ADAMTS14 2 19458
FBXL5 2 19110
SORBS2 2 17563
EME1 2 16070
CDCA3 2 15211
GPR173 2 14624
IL4 2 13773
CPLANE2 2 13405
COL7A1 2 13322
CCDC194 2 13237
FAM72C 2 12421
KIF18B 2 12225
SLC5A6 2 11875
IL6 2 11527
UBC 1 11214
CDK2 1 11180
ISG15 1 11138
RHOA 1 11101

All Genes

ADM5(22238), AR(21690), ADAMTS14(19458), FBXL5(19110), SORBS2(17563), EME1(16070), CDCA3(15211), GPR173(14624), IL4(13773), CPLANE2(13405), COL7A1(13322), CCDC194(13237), FAM72C(12421), KIF18B(12225), SLC5A6(11875), IL6(11527), UBC(11214), CDK2(11180), ISG15(11138), RHOA(11101), SPANXB1(10996), UBB(10963), TROAP(10819), PLK1(10711), APCDD1L(10510), CDK3(10494), PRDM10(10380), TP53(10335), KDR(10224), ERFL(10166), HDAC1(10135), ONECUT2(9964), NCOA4(9743), CDK1(9631), LRRK2(9514), MBOAT7(9489), SEC61A2(9350), ZIC2(9326), CDK16(9153), BCL2(9067), TICRR(9054), GPR78(8853), TMEM150C(8790), EIF4EBP2(8730), CAD(8625), HES7(8584), CDC42(8584), SPATA18(8503), TSPO(8403), CPA5(8295), ANAPC7(8101), PABPC1L(8077), EMX2(7982), IFT20(7957), RIPK4(7938), JUN(7839), SLC16A12(7748), TRAIP(7711), TEDC2(7698), PTX3(7687), AC069503.2(7665), ATXN7L2(7652), CLTRN(7643), CRB3(7439), HES7(7434), SELENOP(7384), PIF1(7294), SRC(7229), METTL7A(7156), NFKB1(6973), RAC3(6900), ITGA8(6744), DLX4(6702), CCL7(6550), MYC(6464), MAPK3(6462), FAM72B(6425), DONSON(6282), HJURP(6267), POTEJ(6194), INS(6179), TLCD1(6022), SIGLEC6(5993), EPHB2(5919), KLRC2(5874), POTEI(5861), ACTC1(5754), AC138969.1(5728), NUMBL(5685), AMH(5645), SNHG28(5630), RHOBTB3(5547), GABBR1(5517), MXD3(5484), SAGE1(5403), REM2(5396), B3GNTL1(5348), STX1A(5339), C1orf94(5330), FAHD2A(5298), HSPA8(5273), AC008687.4(5210), CTNNB1(5201), SPANXC(5105), FAM20A(5059), PSRC1(4960), CKAP4(4719), ZNF117(4694), PANX2(4608), TPRG1L(4607), AC018630.4(4560), GBA3(4559), VAMP3(4511), PTPRB(4511), SAPCD1(4465), CAT(4312), COPS7B(4266), BARX1(4252), WDFY2(4250), SPRR2D(4147), DSCR9(4119), ASIC3(4096), CFAP45(4093), ACTA2(4093), C4orf3(4049), PTEN(3942), NUF2(3935), OR13A1(3901), NFKB1(3896), TBP(3887), LIMCH1(3876), POTEI(3863), FBF1(3845), C20orf141(3833), EPHB2(3832), CDRT15(3790), ERICH5(3750), AC092143.1(3733), RSKR(3725), POTEJ(3717), EMCN(3706), SRC(3698), CCR10(3696), RHNO1(3692), AKT1(3624), NCKAP5L(3623), GOLGA6L9(3557), PLPP3(3549), CCL7(3500), SLAMF9(3497), YARS1(3488), IGF1R(3483), RHOU(3483), AMOT(3465), HSPA8(3450), GGT2(3435), C9orf163(3434), PLXNB3(3432), CRABP2(3372), RAC3(3371), PYY2(3362), Z84492.2(3358), GART(3345), LRP8(3341), ACTB(3319), CCDC154(3271), KAT2A(3251), EP400P1(3236), CRPPA(3175), TMEM81(3146), RHOU(3135), YARS1(3105), PDGFD(3083), RHOB(3053), ITPKA(3040), RHOV(3039), CCL22(3012), MAGEA5(2996), RECQL4(2987), CALB2(2983), FLT3(2972), IGFL3(2960), MOCOS(2951), RAD51D(2933), TNF(2889), USP17L8(2884), LBX2(2878), RAC1(2827), ANKLE1(2770), ITGA6(2767), SARS2(2767), PRKAG3(2757), CHRNA9(2691), FOXM1(2686), SMIM24(2678), CYP3A7(2651), AC138969.1(2651), SPACA6(2641), MOB3B(2630), CSF3(2622), PYCR1(2620), SNF8(2593), ANHX(2572), PTPRB(2567), TTC32(2561), ALB(2555), RABL2A(2554), FAM209A(2547), ACTG2(2533), RSKR(2521), DMRTC1(2503), MAPK1(2493), RGS20(2492), C17orf50(2448), SLC18A3(2411), CNTNAP1(2395), AJAP1(2390), RAMP3(2388), MATK(2382), OBP2A(2378), TMEM138(2285), MMP24(2238), CAVIN2(2237), SLC40A1(2231), AKAP8L(2230), SORBS1(2227), KISS1(2206), SCX(2192), AGAP9(2189), HBP1(2188), FOSL1(2155), METTL24(2150), HS3ST3A1(2119), MGAM(2105), HRAS(2098), SLC7A5(2090), OTX1(2077), OTOF(2073), C6orf141(2056), KRTAP2-3(2056), ZSWIM2(2052), ACTL6B(2038), NFE4(2020), CENPBD1(1982), GAPDH(1955), JPT1(1954), TEK(1953), DBH(1937), STAT3(1915), FOS(1911), ACTBL2(1909), SLC2A9(1878), RHOB(1872), NRAS(1870), AL163636.1(1861), AC006254.1(1860), FGF17(1824), SSPOP(1818), GSDMB(1816), INAFM2(1812), MARS1(1799), SLC38A5(1795), KRTAP22-2(1768), TEX29(1766), NKAPD1(1750), PDE4D(1743), ANK3(1728), WFDC10B(1718), CDK5(1709), ZNF836(1651), UBE2S(1651), FAM53B(1648), INSR(1647), SOWAHB(1638), DENND4C(1623), CDKN1A(1618), SYCE1L(1616), CRP(1598), RHOQ(1579), LINC00313(1560), LINC02870(1542), HDAC9(1524), AL157935.2(1489), OSBPL1A(1489), IMPA2(1481), LILRA4(1479), GFPT2(1479), PTPRG(1476), ARMH1(1471), TOP2A(1466), EXOSC1(1448), FGF2(1441), KMT5A(1435), FLT3(1420), ST13(1416), CT45A8(1403), KPTN(1396), TMEM86B(1391), ADCY10(1383), RXFP1(1374), ZHX1-C8orf76(1372), UMPS(1369), MKRN3(1360), SPANXN1(1353), KLRC2(1342), CD1E(1321), UFSP2(1317), CERCAM(1309), GCK(1307), ATP6V1FNB(1306), FAU(1297), OAS2(1286), CDK6(1281), CORO6(1280), MAPK14(1268), LYRM7(1267), ASNS(1261), NPEPL1(1259), LRFN1(1258), RIT1(1244), SLC12A8(1206), DDX11(1185), KDELR3(1177), FRMPD2(1172), ABCC10(1158), ASNS(1137), SAPCD2(1124), SPIC(1119), MSTO1(1111), FOXL3(1108), RAP2A(1098), GPR162(1096), HACD1(1095), CDC7(1072), ATP8A1(1060), AURKB(1054), CDCA7(1044), OASL(1041), TNNT1(1027), PRKCG(1019), LYPD5(1012), STEAP1B(1008), FOXA2(991), PLIN4(989), KBTBD3(985), HNRNPCL4(980), PMF1-BGLAP(978), GNAO1(972), ATP2A1(967), PEX5L(955), GNB3(941), MAP6D1(941), F2(936), ZNF366(934), TPBGL(931), SGK1(926), HSP90AA1(924), MPV17L(919), CRADD(918), DMRTA1(916), CHCHD2P9(915), KRAS(915), GATA1(914), HSPA1L(912), POP5(907), GATA4(905), PINK1(900), DESI1(899), FCER1A(888), GIMAP6(884), GDF5(868), HOXA2(867), RAD51B(860), ZNF658(854), KRT79(839), KIAA1191(838), LPAL2(837), SP5(832), TUBB2A(829), CARS2(814), RBM3(812), KMT5A(808), GLI3(807), MLLT11(801), TRAPPC2B(793), RSPO4(790), HHLA2(786), MAGEA4(784), CA5B(780), UBL4B(779), EFCAB11(777), SPANXA1(768), C1QTNF8(760), STRADA(760), SCGB1C1(754), CD8B2(751), KBTBD11-OT1(736), COL21A1(735), CPXCR1(734), KRT39(734), RHEB(733), CHI3L2(730), CHTF18(729), MAPK12(725), C4orf19(724), KRTAP16-1(724), NPR3(720), CNTNAP1(719), SGK1(718), SLC10A2(712), KCTD16(710), TAFA3(710), RET(707), PDGFRB(702), STEAP3(700), TMEM158(695), MARS1(694), ITGA2(682), DEFB104A(681), TMEM200C(678), ULBP1(668), PLA2G2A(666), PTH(662), UTY(653), TNS1(648), AC079594.1(648), TPSB2(644), KLK11(639), RABL2B(638), RAP2B(637), SCN10A(632), FABP12(630), POFUT2(623), ESR1(618), FYN(616), ANKRD13D(612), PRKAR2B(609), RGS17(600), DIRAS2(598), NCR3LG1(597), AUP1(596), FBXL3(594), RHOQ(589), BCL6(586), TFAP2E(583), ADCY2(580), USP27X(567), FAM72D(564), ACTRT1(564), RNF41(558), SPEG(556), FBXO43(556), AKT3(549), PLPP5(546), GRIN3B(545), FEZF2(545), RPP40(538), ENGASE(538), EBLN1(536), EGFR(536), TSPY4(532), BIVM-ERCC5(531), HSPA1A(531), CNOT6L(530), ARHGEF37(529), CCDC166(529), C11orf45(526), BCL2L1(526), NBEA(524), LZIC(522), P2RY8(521), AC099811.2(516), PRKN(515), EPOP(511), MSH5-SAPCD1(511), FGFRL1(508), PCNA(507), RFLNA(505), ZNF583(503), SIX2(498), FOXP2(497), TMEM159(493), CILP(492), MAT1A(492), KRT75(488), TPSD1(486), RNF183(486), FLT1(479), AL035460.1(474), FOXL1(473), RAP2C(472), STK11(468), KCND1(466), ACTL9(466), FBXO48(464), SPATA31A1(460), SFN(459), AL121594.1(458), HDAC3(458), DCBLD2(452), PGPEP1(451), SERINC4(450), AC008758.6(449), TANGO6(447), MX2(446), RIN2(445), RGS20(444), RUNDC3B(441), MPP1(441), RGS17(440), MATN1(439), GIMAP6(437), ADIPOQ(434), A3GALT2(433), PDK4(433), AL163195.3(430), MELTF(429), CYYR1(428), FRMPD2B(427), MAP3K7(424), DRD5(419), GSG1(418), ERFE(417), ALDH3A2(414), TCEAL1(413), WNT5A(410), TTC32(410), OR4F5(410), IQGAP2(408), UCN2(406), FRMD5(399), NPIPB9(397), TCF7L2(395), ZNF658(394), CCER2(389), ACTRT2(387), MMP12(385), DNAAF6(383), SLC2A6(380), AC073610.2(379), DNAJC10(379), ELAVL1(376), MAGEC2(374), SCGB1C2(365), KLHL36(362), KRTAP4-16(362), GCK(362), SRCIN1(358), NIPAL3(352), KIAA1549(351), OR2B6(348), HDAC8(347), PECAM1(345), RHOBTB1(343), ZNF404(339), BBS4(338), MSH3(333), SYCE2(333), KCNIP2(329), RAVER2(329), CSF2(329), TMEM191C(328), UBL4A(328), KIF23(327), RERG(325), DNAJB1(324), SHISA9(324), GNL3(319), TTC1(317), XRCC3(317), IDUA(316), RNF13(315), TMCC3(313), PLIN1(313), CLDN4(313), GGT2(313), MYADML2(309), C2orf66(306), CTAGE8(304), OR10A6(304), RHOBTB2(302), AC036214.3(301), SLC12A8(301), FOSL1(299), DHRS3(298), CRACDL(295), ADH5(295), COL22A1(286), SLC25A37(285), CCNF(285), CPSF1(284), TDRD7(284), ABCB4(282), OTOF(282), ERBB3(281), CDK17(279), DUX4L9(276), OXT(274), STIMATE-MUSTN1(274), PTK6(273), TMEM132A(272), OR11H7(272), RERG(271), GOLGA8B(270), PRKAG1(268), OIT3(267), H3Y1(267), CDK15(265), FDCSP(261), GLI2(261), TIGD1(260), HOXA2(260), ZPLD1(259), NAT9(259), RNF19B(258), CPNE7(257), FAM227A(257), POTEE(257), FKBP9P1(256), COL22A1(251), PEDS1(250), ACTL8(248), EDNRB(248), IKBKE(248), MEP1A(247), EHMT1(247), PLA2G10(245), PRAMEF25(244), C4BPA(243), TMEM192(243), OAS1(241), SAA1(241), NUDT17(240), ZNF880(238), CHD1L(237), TSLP(236), IRX6(236), FUCA1(236), LRP5(234), PLS1(232), FKBP1C(231), BANF2(230), TAF10(230), FOXD3(229), RTEL1-TNFRSF6B(228), TMEM220(226), MAPK6(225), NAA40(224), CCDC189(223), RAB9A(218), ANKRD33(218), C9orf85(215), AC006486.1(215), F2RL3(214), CU639417.1(214), RANGAP1(213), VSX1(212), KLF6(212), AC005154.5(211), KALRN(211), SLU7(211), MAP7(210), CCDC85A(209), DGKK(209), FOXC1(207), COL20A1(206), CYP2C9(206), PEX6(204), AC009163.3(204), SLC2A6(204), BORCS7(203), KIAA1671(203), LTV1(202), PPP1R12B(201), MET(200), FGFR2(199), OR7A10(197), VNN3(196), THSD7B(195), RRAS2(195), BCL2L2-PABPN1(195), MYB(194), H2AX(193), SLC35E4(192), HMSD(190), UPK3B(188), TPBGL(187), CNTNAP5(186), REEP2(185), AC003688.1(185), ZNF521(185), JAK1(184), FAM218A(183), FGFR3(183), ERV3-1(181), KCNN4(181), CHRM3(181), CDY1(181), ACTR10(179), MRAS(179), UCN(179), ZIC5(178), NPIPA9(178), DECR1(178), PPP2R2C(177), CAMKV(176), NBR2(176), PLAC1(175), ZNF320(175), MYH14(175), USB1(173), PCDHGA9(172), SPTBN1(172), LRRC38(171), RXFP3(171), SPANXD(171), ERMN(171), ELN(170), LAMP5(170), CCNDBP1(170), LHB(169), TOMM34(168), RBIS(168), PCBP4(166), MAT1A(165), COQ7(164), SRCIN1(164), MDGA1(163), FAM174A(163), PPP1R3D(162), PCDHA11(162), MRGPRX2(160), AC091167.2(160), DUX4(159), AL109827.1(158), KRTAP13-1(157), RASD1(157), LSMEM1(155), MT1G(154), TXLNA(153), HSPA5(153), FAM166C(152), EHHADH(152), SLC3A1(152), NOP2(151), HACD1(151), C4orf33(149), ATOH8(149), GPAT2(149), UBE2D3(149), C10orf90(148), ABHD6(147), KIR2DL4(147), ZNF843(147), CTSG(145), ROBO3(145), CFAP298(144), PLEKHF2(144), OTOA(143), GATA3(142), C11orf58(141), FOXO6(141), ITGAE(141), RAPGEF4(141), ABCG2(140), MARCHF4(139), CHRD(139), ATP2A3(137), TRAPPC2(136), CYP21A2(136), IL23A(136), SFN(134), P2RY2(133), CMA1(133), SNF8(133), GNL3(133), PELI3(131), RUFY4(131), IGBP1P2(131), ENSG00000163009(131), OR7G1(130), NOS3(130), MYBL1(130), SEMA3A(129), HSPA4L(129), RND3(129), ZSWIM5(128), C1orf189(128), C16orf97(128), AC005702.1(128), C1RL(127), ROBO3(127), NPIPA1(127), CRLF2(127), TM4SF19-TCTEX1D2(127), PRICKLE4(127), ZFAND4(127), SGCB(126), RPS6KA1(126), UBD(126), ASCC1(125), HIPK4(124), MAGEH1(124), DENND1C(124), SAMM50(124), ASB16-AS1(123), RHBDF1(123), RORA(123), IGFLR1(122), LINC01620(122), CDK14(122), DMC1(121), TMEM47(120), RNF20(120), FAM160A1(120), ZNF879(119), RAD51(118), ITIH4(117), POLR3G(116), CFAP221(116), CCL8(115), AC244197.3(115), RAP1A(115), ACTA1(115), CRPPA(115), AC008878.3(114), AC091167.6(114), TPSG1(113), CST2(113), LINC00242(113), HSPA1L(112), SPRED3(111), AC009690.3(111), ZNF595(111), MT1F(110), C1orf53(110), DCLK1(110), OR10H2(110), PIMREG(109), JAK2(109), NPIPB6(108), KLHL9(107), CDK4(106), NAV3(105), ZNF304(105), LCK(105), DOCK8(104), TCTE3(104), EPB41L4A-AS1(104), FAM72A(104), GYG2(103), DFFA(103), SHOX2(103), PDGFRL(102), FGD5(102), TRPV3(102), PCSK5(102), SLC26A6(102), AC233992.2(101), AC244517.10(100), OGT(100), HGS(99), APOB(99), RPS6KB1(99), PURA(99), OSTN(98), RAPGEFL1(97), LRRC31(97), ELAPOR1(97), LINC00207(97), TTC6(97), COL4A5(97), C3orf35(97), LORICRIN(97), IZUMO4(96), RPS4Y2(96), FAM72A(95), LYPD8(95), ERAS(95), TRIM4(94), L1CAM(94), KAT14(94), ASB16-AS1(94), SCP2D1(91), IGFL2(91), CYP46A1(90), MMAA(90), THAP9(90), SOCS6(90), ARFGAP1(90), ALDH1A1(89), TTLL11(89), WFDC3(89), PISD(88), MOV10(88), BCL2L12(87), FOXD4L6(87), NPIPA1(87), HRH3(86), TF(86), ZNF420(86), LINC02868(85), PCDHGA12(85), MPZL2(84), ATG10(84), CXCL5(84), SNRPA1(84), SPANXN1(84), SLC52A2(82), CLMP(81), SRRM5(81), HEBP2(80), LINC02210-CRHR1(80), NHP2(80), EZHIP(80), ARL9(80), XG(79), TUBB2B(79), RPS27AP5(79), RAMACL(79), TMEM159(79), RPS6KA2(79), KCNN3(79), LBHD1(78), AGAP6(78), MTRNR2L6(78), NSUN5P1(77), TCTE3(77), TUBB3(76), POLR1D(76), CT45A9(76), MERTK(75), SLC25A37(75), LEP(75), FAM218A(75), PGRMC2(74), ACLY(74), WT1(74), NSUN5P1(74), TIRAP(73), KRT27(73), HNRNPCL1(73), EIF4B(73), IL2(73), AC093525.2(72), PDE6C(72), OGN(72), DDX41(72), ID2(71), XPO5(71), WBP1L(71), MROH2A(71), TTTY5(71), PDE6B(71), CHURC1-FNTB(70), IL31RA(70), RNF207(69), GTF2E2(69), MX1(69), CYP3A7(69), TOMM20(69), RNASE13(68), MAPK15(68), TMEM165(67), TOB2(67), PPIAL4C(67), DNAJA2(67), LIN54(67), LURAP1L(66), FASN(66), ATP8A1(66), MEF2B(66), DNAH8(65), THBS3(65), STIMATE-MUSTN1(65), C5AR2(64), RBM45(64), ABRAXAS1(64), SMARCA2(64), HSP90AB1(64), EGR1(64), ANKRD33B(63), SLC1A5(63), IFNG(63), FOXL2(63), SMIM29(63), RAB34(62), SLC26A10(62), SLC31A2(62), CDC20(62), ANXA8(61), TRMO(60), GALNT4(60), RASL10B(60), STEAP1B(60), PLCL2(60), PRKAR1B(60), COL11A1(59), CENPW(59), REM1(59), DHRS12(59), GARS1(59), UNC13A(59), CDADC1(58), ADAM8(58), TMEM191B(58), BCL3(58), SLX1A(57), DENND11(57), GTF2B(57), IFITM1(57), TMEM220(57), AC233992.2(57), CAPRIN2(56), PPP1R32(56), OTUD7A(56), CDK11A(56), ZNF543(56), SRRM5(55), FLRT3(55), PUS1(55), AC005154.5(55), SPATA4(54), AKAP6(54), EZHIP(54), EWSAT1(54), NBPF1(54), LY6G6D(54), HNRNPCL2(54), CCER2(54), RIBC2(53), CREBRF(53), LDLRAD4(53), SETSIP(53), C11orf54(53), ARHGEF28(53), CENPO(52), FOXP3(52), HESX1(52), TSPY1(52), NLRP10(51), AC003005.1(51), TBC1D8B(51), MITF(51), FAM53B(51), ZNF79(51), CXXC4(50), LINC01559(50), CCND1(50), PNPLA7(50), COPS4(50), NIM1K(50), BEX2(49), KIAA1614(49), AC011511.1(49), SEC24B(49), CEP83(49), U2AF1(48), FAHD1(48), QRFPR(48), CUBN(48), KCNAB1(48), POLDIP2(47), EREG(47), ALG3(47), SEC61A1(46), SCML2(46), SAMD1(46), SLC10A6(46), PALM2AKAP2(46), RBAK-RBAKDN(46), TGFB1(46), ITM2B(46), SOCS1(46), FAM13B(45), FAM47B(45), LINC02872(45), WNT3(44), PPP2CB(44), FOXA1(44), NSA2(44), RRAD(44), OR2V2(44), GTPBP2(43), MIIP(43), ABCC11(43), NUDT5(43), UBE2S(42), ASB17(42), STAG3L1(42), ALG1L2(42), CTSO(42), PAX6(42), RAB11A(42), DMGDH(42), HMGCLL1(42), C11orf45(42), AL157935.2(42), POLR2C(41), ZNF576(41), TMEM25(41), C21orf58(41), INAVA(41), GOLT1A(41), NPIPB5(41), CX3CL1(41), EPOR(41), LENG9(41), LMNB2(40), C3orf35(40), COL9A2(40), RHOJ(40), APOE(40), EPHB3(40), ENSG00000213865(39), ZBTB16(39), SHANK2(39), GAGE2A(39), MYO19(39), ORC6(39), AKT2(39), EIF4E3(39), C2orf76(39), TAAR6(38), AGBL2(38), ATF5(38), C10orf105(38), HP(38), URGCP-MRPS24(38), ACHE(38), TMEM245(38), DCST2(38), DSCR4(37), PCDHAC1(37), L34079.1(37), BUD23(37), LINC02872(37), SDR9C7(36), C4orf48(36), SMG9(36), RND2(36), RAD50(36), LDLRAD2(36), AC244197.3(36), CHAT(35), REPS2(35), KIR2DP1(35), KHDC1(35), MS4A2(35), CXCL8(35), CCDC137(35), TLR9(35), STRADA(35), MAST4(34), CFAP300(34), SHISAL1(34), CLDN25(34), HASPIN(34), BOP1(34), RCBTB2(33), MYBL2(33), SLC1A1(33), GEM(33), LONRF3(33), SOX12(33), MAGEA5(33), PRR23D2(33), TMEM135(32), FITM2(32), NPIPB2(32), AC008764.4(32), FAAP24(32), ERICH6B(32), DPAGT1(32), CCL24(31), ANO3(31), UGT2A3(31), NTPCR(31), IGFN1(31), H2BC18(31), PIK3CA(31), OR52I2(31), SMKR1(31), SVOP(30), SOCS3(30), LRRC73(30), TAFA5(30), SPINK8(30), H2BC8(30), LINC01138(30), DNM2(30), TSC22D1(30), SLC20A1(30), FARS2(30), CCDC74A(30), TTC24(30), TUBB7P(30), FOXP4(29), PRSS53(29), CCDC78(29), SERPINI1(29), BBS12(29), ZFP82(29), C2CD4B(29), CCT4(29), ADAM8(29), DIRAS3(29), CXCL1(29), TLN2(29), PRKAG1(29), DHRS7C(29), FAM50B(28), LRRC15(28), SNORC(28), AARSD1(28), REC8(28), C1orf159(28), GIPC2(28), EDA(28), SYNE3(28), EFNA5(28), TEAD4(28), CCNA1(27), LRRC37A3(27), RGS11(27), PTK6(27), KIF18A(27), PDZD2(27), EPHA10(27), EHMT2(27), LINC01089(27), LGALS2(26), STBD1(26), KRT2(26), PNMA8A(26), SPATA31D3(26), GPR33(26), PLPP5(26), PITPNC1(26), AKTIP(26), ADCY5(26), BACE2(26), RHPN2(25), GREB1L(25), CLDN14(25), VCX3A(25), KLLN(25), LIPA(25), CCNI(25), DNASE2B(25), EEF2(25), SLCO2A1(25), LPAL2(25), ACACA(25), CHAC1(24), CCDC81(24), SCFD2(24), ENSG00000269881(24), RTEL1-TNFRSF6B(24), WDR62(24), AMD1(24), CDKN1A(24), EGLN1(24), CARTPT(24), CCDC121(24), MTOR(24), SPACA7(23), GIMAP8(23), AC007731.4(23), CREBBP(23), SLC18A1(23), HDAC10(23), E2F5(23), CARS2(23), IGF2BP1(23), BORCS7(23), PBK(23), OR7D4(23), LINC01138(23), GGTLC3(23), COPZ2(22), RIPOR2(22), MASP1(22), KAAG1(22), MINAR1(22), TMEM270(22), SH2D7(22), CCDC137(22), CFAP73(22), TMEM233(22), GRIN2B(22), APLNR(22), DTX1(22), DCTN3(22), PHAX(22), SIX2(22), RHOD(22), NDUFAF8(22), GJA5(22), ARHGAP10(21), TOLLIP(21), NKAIN4(21), AVP(21), ZNF473(21), ADGRG3(21), ENO1(21), RASL12(21), JAK3(21), B3GAT1(21), TM4SF18(21), CCDC63(21), TRIB1(21), LSM1(21), PIDD1(21), FBXL6(21), RINL(21), ZNF542P(21), AC005726.1(21), FAM74A3(21), TXNDC15(20), GALNT12(20), ANGPTL8(20), NBPF3(20), KLF17(20), IL20RB(20), MT1M(20), DCDC2C(20), TMEM229A(20), GNAS(20), TIMP3(20), RGP1(20), NKX3-2(20), DBH(20), ASB8(20), C17orf107(20), OR8B4(20), FAM86C1P(19), ZFP64(19), HSD17B6(19), GSK3B(19), TTC28(19), ZNF821(19), TCIRG1(19), OIT3(19), USO1(19), NDUFS4(19), MAPK7(19), NPB(19), CTBP1-DT(19), KRTAP4-6(19), LILRA4(19), AL117348.2(19), MAPK8IP2(18), ILK(18), MANEAL(18), PPIAL4A(18), CD40LG(18), SPDEF(18), FOXF2(18), FBXL17(18), ABI3BP(18), SNORC(18), ZNF583(18), KRTAP16-1(18), ZNF812P(18), CNGA4(17), PRDM8(17), GPSM1(17), PWWP3A(17), LLCFC1(17), CTSF(17), SERF1B(17), RALA(17), STN1(17), MFSD1(17), HTR2C(17), PTPN9(17), DNAI2(17), OR51F2(17), CENPBD1(17), SMIM10L2A(17), PKP3(17), FAM200A(17), MGST2(16), LNX2(16), ASTN2(16), SPATA45(16), LINC02817(16), GIPR(16), RNF14(16), FOXN3(16), CARS1(16), REEP2(16), LBX1(16), MAPK13(16), CACNB3(16), ETV4(16), WFDC10B(16), DGAT1(16), CYP26C1(16), ANOS1(15), SLC17A9(15), B3GAT3(15), BTBD11(15), GNG3(15), ZFYVE19(15), WASHC1(15), CSAG3(15), COX15(15), CCDC85A(15), ATP11A(15), PCDH11Y(15), LGALS3BP(15), FARSB(15), TAF1L(15), RALB(15), SAP18(15), PTPRN2(15), LHX8(15), E2F7(15), ADORA2B(15), ZNF570(15), VPS37D(15), OPCML(15), TBC1D26(15), USP17L1(15), PPIAL4E(15), CYFIP1(15), AC091959.1(15), REC8(14), ZNF346(14), SENP8(14), DEFB124(14), SERPINB11(14), LINC01101(14), MYCBP2(14), GSC2(14), EED(14), TP53INP2(14), IL11(14), CSTF1(14), OAS3(14), SOD2(14), PEX5L(14), RAP1B(14), BLK(14), ANK2(14), POLE3(14), AGBL2(14), ZNF622(14), CLEC14A(14), NPEPL1(14), TMEM253(14), PHACTR3(13), BEX4(13), TMEM245(13), ART4(13), CSPG5(13), GH2(13), NARF(13), ARMC12(13), PGAP4(13), FAT3(13), MXRA7(13), AC008878.2(13), FGFR1(13), TUSC3(13), MT2A(13), BOLA3(13), ARHGAP42(13), TRMT61B(13), OR5B2(13), ROR1(13), SEMA3G(12), PRLH(12), CEMIP(12), DHDH(12), BST1(12), BCL11A(12), CPA4(12), PCDH8(12), DMRTA2(12), LGI4(12), VOPP1(12), PWWP3B(12), TRARG1(12), IPP(12), MUC21(12), CABP7(12), HIF1A(12), APEX1(12), CDS2(12), PGK1(12), GSG1(12), HHLA2(12), ALG5(12), RRP36(12), ZIC5(12), HSPG2(12), PAXX(12), ADPRHL1(12), ANKRD33B(12), PRKACG(12), CATSPER2(12), P2RY8(12), OLIG1(12), RPL23AP82(12), CCK(12), RTP5(12), DENND1C(12), PARP12(11), PIK3R1(11), LYSMD3(11), HPDL(11), MT1X(11), SBSN(11), KRTAP4-8(11), AL139300.1(11), AC090227.2(11), FAM136A(11), MEF2A(11), SIGLEC6(11), SLC12A7(11), RAPGEF5(11), PRKG2(11), TMEM47(11), RHPN1(11), SPRR2D(11), CRYL1(11), ANKRD33(11), NR0B1(11), CES2(11), OR52A4P(11), ANKRD34C(11), MKS1(10), CABP7(10), PLP1(10), GAL3ST2(10), C15orf48(10), SSX6P(10), MIR7-3HG(10), C1orf194(10), FOXD4L1(10), LIPI(10), DEFB115(10), SORBS1(10), DNAJC2(10), ACTR1B(10), CENPA(10), NFYB(10), PI3(10), ARHGEF16(10), ADCYAP1(10), GAREM1(10), ADPRH(10), SST(10), ATP2A2(10), ERFE(10), EDDM3B(10), CHEK2(10), SLC6A9(10), LINC01011(10), INAFM2(10), SMPD3(9), MLPH(9), PPP1R1A(9), PKIB(9), IL17RD(9), MXRA8(9), SSMEM1(9), KAT5(9), PLGLB1(9), NRN1L(9), KRTAP9-3(9), HLA-DQA2(9), AC018755.2(9), CACNG3(9), DMRT3(9), WNT3(9), KIF20A(9), CCNG1(9), PECR(9), CD207(9), PTGER2(9), KHDRBS3(9), IGF2BP3(9), CBX8(9), KIF2C(9), AQP10(9), DIP2C(9), CPT2(9), SHH(9), OR5I1(9), TUBB6(9), BNIP3(9), CYBC1(9), SYN3(9), TPSB2(9), OR6C3(9), ADGRG1(9), MMP12(9), ARL14EPL(9), CEACAM4(8), DKK1(8), TREM1(8), OSR1(8), OLAH(8), PID1(8), BPNT1(8), ART5(8), FBLL1(8), HLA-DQB2(8), LRRC37A2(8), ANK1(8), PRKACA(8), USB1(8), GRB10(8), EIF2B1(8), RNF19B(8), PROX1(8), HOXC11(8), SLPI(8), GSTM1(8), STK26(8), PSAT1(8), GCHFR(8), ACTR1A(8), TARBP2(8), ESD(8), ERBB2(8), SAMD1(8), SNCA(8), NOTCH1(8), FGF17(8), CCDC78(8), KCNK5(8), SENP8(8), PUSL1(8), S1PR1(8), ZNF404(8), ZBTB8OS(8), FKBP9P1(8), RIMKLA(8), APOLD1(8), MKRN3(8), SLC2A4(8), ODF3L1(8), SETD3(8), VSIG10L(8), EIF4EBP1(8), LCTL(8), CLDN4(8), ZNF836(8), L1CAM(8), FOXO6(8), AL354761.1(8), AC026954.2(8), AC005020.2(8), HIPK2(7), PCDHB15(7), EVA1A(7), CCDC91(7), PODXL(7), ATP8B3(7), TRIM43B(7), OTULINL(7), CCZ1B(7), ZC3H12C(7), FOXD4(7), HAS2(7), DENND2C(7), SLC25A22(7), SP140L(7), PRG2(7), LYPD6(7), TRNP1(7), RPS10-NUDT3(7), PRKCQ(7), TRIP13(7), TMEM38B(7), KLF5(7), PRX(7), CREB3(7), NEK2(7), ECRG4(7), KDSR(7), SPRYD7(7), PODXL(7), DAB2IP(7), PIM1(7), CFAP300(7), TM4SF19(7), FADS1(7), SKA1(7), KCNJ15(7), C1R(7), PGAP4(7), FRMPD2(7), PRKCE(7), GTPBP2(7), OR2T1(7), YES1(7), CLVS1(7), RPS6KA3(7), IFNL1(7), IQGAP3(7), C1QL4(7), SAXO2(7), NPIPB9(7), ZNF658B(7), CALM1(7), GPATCH3(7), R3HDM4(7), BTBD17(7), GIMAP1(7), LINC00115(7), CYP21A2(7), FAM90A20P(7), ZNF487(7), ABCA11P(7), ZNF723(7), DCP1A(7), H2AB1(7), SLC11A1(6), MAGEA10(6), MALL(6), MT1E(6), TRAPPC12(6), RBM20(6), RTL8B(6), PCDHGC5(6), CGB1(6), ENSG00000228439(6), PLPP1(6), GTSE1(6), AAAS(6), MSLN(6), MAP3K8(6), NEIL3(6), GLI1(6), PDE4D(6), ACTR8(6), ZFP30(6), TBC1D15(6), STX16(6), RPP40(6), NEDD8(6), HAUS8(6), CCNA1(6), RXFP2(6), KATNBL1(6), PPP3CA(6), HSPD1(6), ACTL7B(6), MMAA(6), RIT2(6), FAM81B(6), NPR2(6), GMPS(6), MSS51(6), HSP90B1(6), LINC00305(6), CYB5D1(6), F8(6), AJAP1(6), ZBTB12(6), ALG1L2(6), KBTBD11-OT1(6), BFAR(5), PYROXD1(5), BOD1(5), KCNJ15(5), CBS(5), CST1(5), TCP11L1(5), SLITRK2(5), FSCN2(5), S100A16(5), MMP1(5), H2AC19(5), TBC1D3(5), PPP5C(5), ZC3H3(5), PLEKHA5(5), NOA1(5), DNM1L(5), ZNF14(5), CPZ(5), MRPL18(5), RAB38(5), MYOD1(5), FKBP11(5), RAB33A(5), TRMO(5), SEMA7A(5), CARD14(5), ARHGEF19(5), UCK2(5), SNX30(5), CNBD2(5), RHBDL2(5), SHROOM4(5), OR3A3(5), ATAD3B(5), HELQ(5), CPA3(5), ZNF704(5), DDIAS(5), NPR1(5), KISS1(5), GIMAP8(5), XCR1(5), RUVBL1(5), CSTF3(5), BDNF(5), BASP1(5), LRRC37A3(5), SIX5(5), MAPK11(5), ZNF699(5), C20orf204(5), C1orf122(5), KPRP(5), ARSH(5), COLQ(5), LINC01588(5), SBK3(5), HGH1(5), AF241726.1(5), PPBPP1(5), AC007998.2(5), EPYC(4), CAPS(4), PRUNE2(4), WFIKKN1(4), POPDC3(4), RMDN3(4), CHODL(4), LALBA(4), GSDMA(4), DNASE1L2(4), BTD(4), GOLGA6L2(4), CD164L2(4), SCN4B(4), NPAP1(4), BCO2(4), SULT1C4(4), NSUN6(4), TNFSF12-TNFSF13(4), AC004691.2(4), TBXA2R(4), CELSR3(4), JADE2(4), HHAT(4), METTL22(4), ACTL6B(4), PHLPP1(4), ABL1(4), RASD2(4), CDKN3(4), SEL1L2(4), RP1(4), GSR(4), THEG(4), HAMP(4), DOCK8(4), FGF12(4), GUCY1B2(4), KCNS1(4), DTNA(4), AMHR2(4), NEK3(4), RHOF(4), ABL2(4), MEPCE(4), STK32B(4), C9orf85(4), CFAP161(4), KIT(4), PLA2G4D(4), CALHM4(4), TMEM135(4), NPIPB3(4), HSFY2(4), TRABD(4), UGT2B7(4), KLF17(4), UBQLNL(4), LMNB2(4), PFN4(4), OR2T8(4), HNRNPA0(4), GLIPR1L2(4), ZNF792(4), METTL23(4), LINC00471(4), ZNF329(4), ACTL10(4), NTM(4), TLCD2(4), NDOR1(4), ZBED6CL(4), HSH2D(4), ENTPD6(4), TUBA3C(4), RPS6KL1(4), SP5(4), TMEM191C(4), RNASEK(4), DUX4L9(4), SSU72P8(4), CCDC192(4), ZSCAN31(4), PABPC4L(4), SAA2-SAA4(4), AC092718.3(4), SPANXN2(4), COMMD3-BMI1(4), FAM25BP(4), DUSP14(4), OR6Q1(4), PPIAL4F(4), METTL22(3), ARHGAP4(3), TLL2(3), KIAA1549L(3), SLC25A23(3), EML2(3), DCST2(3), SLITRK5(3), SDHAF2(3), NCBP2L(3), C2CD4C(3), FAM110C(3), KRT5(3), RD3(3), MACO1(3), KRTAP3-2(3), LBH(3), ENSG00000213865(3), ENSG00000262621(3), CD9(3), CTNNA1(3), ANAPC4(3), GYG2(3), SNAP91(3), SMARCD1(3), PDK3(3), VPS35(3), SEMA3A(3), SLC46A1(3), TYRO3(3), EZR(3), CREM(3), NCR2(3), IZUMO4(3), HNF4A(3), SALL4(3), CDADC1(3), ACP5(3), RIPK2(3), FGF6(3), IL17A(3), PERP(3), TBX18(3), TBCCD1(3), MMP8(3), KLF9(3), MTERF2(3), KLHL7(3), TREM1(3), SRMS(3), FLNC(3), KNSTRN(3), LBP(3), PGPEP1(3), OLFM1(3), SHFL(3), ABCB7(3), LGR6(3), TTC9(3), C9orf40(3), WDR38(3), RHBDL3(3), BCL10(3), PRKACB(3), AFF3(3), CPXCR1(3), CLCA3P(3), GNA14(3), CD1E(3), CCDC24(3), C16orf86(3), GNE(3), GPSM1(3), RECQL4(3), DHRS3(3), IL31RA(3), ADCY1(3), AMOTL1(3), TEPSIN(3), VASN(3), GBX2(3), ASPSCR1(3), BTD(3), SP7(3), PPM1D(3), POLR1C(3), RXFP1(3), RND1(3), C1QTNF1(3), SUGCT(3), CCDC57(3), ACBD7(3), GAK(3), GJD3(3), FAM9A(3), KCTD16(3), CCR4(3), ACTG1(3), CRELD2(3), C1QTNF8(3), HSF1(3), SPATA31A6(3), CYP4F12(3), KRT10(3), FAM25A(3), FBXL22(3), AL662899.1(3), ZNF616(3), FBXO48(3), KRTAP5-6(3), TSGA13(3), PPM1N(3), SYCE3(3), PIGBOS1(3), DEFB130A(3), SPTY2D1OS(3), TRIM39-RPP21(3), AC069368.1(3), ZNF718(3), HOXA10(3), C1orf210(3), ALG11(3), CTSO(3), KLRA1P(3), AL355916.3(3), AC107871.1(3), AARSD1(3), AC090004.1(3), TEX28(3), MYO19(3), FP565260.6(3), AGK(2), GPRC5A(2), Z83844.1(2), MYLK2(2), C3orf14(2), PIGZ(2), ORMDL1(2), KLF4(2), CMTM7(2), TSPAN7(2), FBXO27(2), PYGO2(2), SYNPR(2), OTOP1(2), MZB1(2), TPSAB1(2), C2CD2L(2), GPR139(2), CFAP65(2), CIB1(2), TAL2(2), CCDC9B(2), LYPD2(2), C1orf174(2), FOXD4L5(2), LTC4S(2), PRAMEF11(2), AL672142.1(2), ZNF350(2), ZNF2(2), CCL18(2), ENSG00000281028(2), ENSG00000274897(2), MYLIP(2), GPRC5A(2), RETSAT(2), HERPUD1(2), PITX1(2), CHAT(2), SPAG5(2), ZNF416(2), PGS1(2), ASAP3(2), DNMT3B(2), MCOLN1(2), ZFHX4(2), COMT(2), PIM2(2), NDFIP2(2), HSDL1(2), SPAG1(2), SLC1A6(2), URI1(2), PDCD5(2), APLP1(2), MEIS3(2), IMPDH1(2), MEST(2), PSMD11(2), YWHAE(2), SH3D19(2), RAPGEF2(2), CREBL2(2), CD83(2), IL12B(2), PPP2CA(2), PRKAG3(2), IL1RL2(2), GADD45A(2), ARTN(2), HS1BP3(2), ELOVL3(2), RPL21(2), PRXL2A(2), EEF1E1(2), IL1B(2), GRIA3(2), UROD(2), RRAS(2), AUNIP(2), RIBC2(2), FEZF1(2), HOXD10(2), TRPM4(2), SLX1A(2), KMT5C(2), VRTN(2), KLHL36(2), TTLL4(2), EDAR(2), MMD2(2), POLR1E(2), KLC4(2), UQCC2(2), SMAD6(2), LNX2(2), TRIM65(2), SLC47A1(2), C1orf216(2), PFDN2(2), RORC(2), HHIPL2(2), NFKBIZ(2), TRIM4(2), NXF3(2), CETN2(2), FAM83A(2), NFIB(2), INIP(2), PAOX(2), SAA4(2), HMGA2(2), ADGRL3(2), HNMT(2), AKAP6(2), PTH(2), RETREG1(2), CNOT8(2), KCNMA1(2), TSPAN7(2), NSMCE2(2), PHKG2(2), GAREM2(2), KCNB1(2), CD1C(2), PAQR6(2), SPC24(2), TMEM82(2), SMCP(2), TRIM46(2), CCT3(2), CXCL5(2), H2AZ1(2), NUDT2(2), C1QL3(2), WDR72(2), YWHAB(2), DNAAF3(2), AC011511.1(2), BEST1(2), ATG4B(2), LINC01620(2), CXXC4(2), ATF5(2), OTUD7A(2), KLF13(2), CAVIN4(2), HTRA3(2), CYP4F22(2), HSFY1(2), NMNAT1(2), CD7(2), CNIH2(2), CABP4(2), LYSMD3(2), CALHM5(2), PRM3(2), PRR26(2), IGIP(2), MX2(2), ARSI(2), DNAH2(2), PRKX(2), A3GALT2(2), XPOT(2), UBE2G2(2), PRSS57(2), RGPD2(2), HGS(2), KRT79(2), ZNF829(2), CD300E(2), ACTL7A(2), KRTAP21-1(2), GPR21(2), IGFL3(2), PLEKHG4(2), ZXDA(2), ZNF568(2), C1orf53(2), MACO1(2), FKBPL(2), HSPA1B(2), MAS1L(2), PCDHA1(2), CRYGS(2), LTB4R(2), DENND10P1(2), TIGD1(2), UBA52(2), FAM30A(2), PRPS1L1(2), TSPAN19(2), CXorf51B(2), NME2(2), USP51(2), AC005324.3(2), EID1(2), MTRNR2L10(2), AL049844.1(2), POC1B-GALNT4(2), TGIF2-RAB5IF(2), CDC37P1(2), BOLA2-SMG1P6(2), SRSF8(2), GDF2(2), CSAG3(2), HEATR9(2), Z84492.1(2), AL024498.2(2), AC092587.1(2), USP27X(2), FP565260.1(2), C11orf98(2), HS3ST1(1), ZNF263(1), CYB561(1), SLC7A14(1), STMN4(1), GABRA1(1), NOP58(1), STYK1(1), DDX3Y(1), ATP2B3(1), HDAC4(1), TFRC(1), CD5L(1), PTGS2(1), NSF(1), TUBE1(1), RBM7(1), UBE2T(1), KCNN2(1), NDC80(1), CXCL2(1), CDC14B(1), ABCB1(1), CPNE3(1), GNAO1(1), IGBP1(1), PRTFDC1(1), RHBDD3(1), NEFH(1), LGMN(1), PYGB(1), SGK2(1), SLC17A9(1), CDC25B(1), TRIB3(1), CSNK2A1(1), PROKR2(1), HCK(1), PCSK1N(1), MAGT1(1), RGCC(1), N4BP1(1), ARL2BP(1), CCL22(1), EARS2(1), CPQ(1), FCGRT(1), IL4I1(1), HOXA1(1), HOXA3(1), PRKAG2(1), PRUNE2(1), AK1(1), GTPBP4(1), RECQL5(1), HLF(1), SULT1E1(1), PF4V1(1), INPP4B(1), HGFAC(1), LTA4H(1), LTBR(1), CMAS(1), BAG2(1), SEMA5A(1), FAM172A(1), GNPDA1(1), CHMP3(1), PASK(1), PIK3R3(1), HSD11B1(1), RPA2(1), HMGN3(1), ZC2HC1C(1), TCTN3(1), SFRP5(1), TNN(1), IQSEC3(1), KBTBD7(1), LIAS(1), RASL11A(1), HS3ST2(1), FAM124B(1), MC3R(1), FAM210B(1), KCNK17(1), NRN1(1), RAB17(1), CXCL6(1), GPR108(1), TNFSF14(1), L3HYPDH(1), MASP1(1), TUBA4A(1), ORMDL1(1), CALML4(1), EPB41L4A(1), NCAN(1), MNX1(1), MED18(1), KREMEN2(1), CDK8(1), C1QTNF6(1), ACTR3B(1), GSC(1), CATSPERB(1), PLEKHA8P1(1), SAA2(1), ANO3(1), KCP(1), TEC(1), MDM2(1), RCBTB2(1), ZDHHC4(1), CALCOCO2(1), CDK9(1), ARPC5L(1), TLR2(1), C11orf1(1), MMP13(1), HERC3(1), C1RL(1), ESR2(1), SCAPER(1), SPATA22(1), WNT9A(1), PHLDB2(1), PLA2G7(1), TMEM140(1), FAM135B(1), HMCN2(1), CNNM2(1), B3GAT3(1), GPHA2(1), LYPD1(1), DIXDC1(1), PRSS53(1), ANO4(1), INPP1(1), PABPC3(1), PELO(1), CLGN(1), PTPRR(1), CD8A(1), SPHKAP(1), CYP2U1(1), C2CD6(1), MPV17L(1), FCHO2(1), CNOT11(1), ABCG1(1), DVL3(1), TNFSF13(1), PPP1R32(1), TSSK3(1), NFIA(1), SNX7(1), C1orf74(1), ZSWIM2(1), TCF23(1), SMIM12(1), RHO(1), METAP1(1), HPGD(1), HHIP(1), F2RL1(1), CSF2(1), CREBRF(1), EN2(1), MICALL2(1), YWHAZ(1), NLGN4Y(1), STK32C(1), PTER(1), ADAMTS15(1), TK2(1), TMEM170A(1), JSRP1(1), ZNF526(1), TBX10(1), OR1F1(1), GNG4(1), TNIP2(1), GCSAML(1), CA5B(1), BCRP2(1), CALML6(1), NPAS2(1), SOCS6(1), TPD52L3(1), KRT13(1), ZNF561(1), OR8J1(1), CBWD1(1), ANKRD13D(1), RELA(1), DELEC1(1), AC097637.1(1), FAM166C(1), LRFN4(1), RGMB(1), C12orf76(1), B4GAT1(1), SLC66A1L(1), OR5J2(1), FOXR1(1), ZSCAN2(1), GNG7(1), CNTD1(1), LY6H(1), MTHFR(1), FAM210A(1), OR2M7(1), SLC25A22(1), IMPDH2(1), GEN1(1), RNF186(1), FBXO34(1), C3orf38(1), CCDC89(1), PLD6(1), DCTPP1(1), C3orf80(1), MIGA1(1), MB21D2(1), ZFP3(1), OR56B4(1), GPR62(1), TCEAL8(1), NPM1(1), WASHC1(1), P2RY13(1), MCEMP1(1), TREX2(1), DGCR6(1), GPR1(1), IQCF2(1), ACTRT3(1), LRRC19(1), ZFP1(1), C6orf58(1), H2BC21(1), DRD1(1), DMRTC1B(1), RAB11B(1), SHC4(1), POU3F1(1), ARL17A(1), TMEM210(1), NAP1L2(1), C17orf58(1), OR10H1(1), TRABD2A(1), PCDHB13(1), SBK2(1), NHEJ1(1), ARL4C(1), DUSP21(1), CGB5(1), DCAF8L2(1), FAT4(1), CTSE(1), WDR5(1), HDAC2(1), DYNC1H1(1), KCNMB2(1), SCGB1D4(1), UGT2B17(1), SULT1C4(1), ZNF813(1), ZXDB(1), SH3BGRL2(1), ANKRD13B(1), OR10Z1(1), RAET1G(1), RPL12P1(1), PJVK(1), SKIV2L(1), TRIM13(1), TMEM240(1), TMEM88B(1), C11orf91(1), LGR4(1), KRT6A(1), MANSC4(1), CYS1(1), CSNK1E(1), AMZ2P1(1), IQCF6(1), C12orf71(1), MTCP1(1), CXorf49(1), TENM3(1), UMAD1(1), ZNF826P(1), TWIST2(1), LINC02817(1), HNRNPUL2-BSCL2(1), FAM237A(1), SPAAR(1), LINC01554(1), TMEFF1(1), TUNAR(1), TMED7-TICAM2(1), FOXD1(1), INMT-MINDY4(1), PCDHA3(1), LY6G6E(1), PRECSIT(1), SMIM10L1(1), MTRNR2L1(1), KLRF2(1), RPL36A-HNRNPH2(1), AL136295.3(1), AC138894.1(1), OR1D5(1), RBM8A(1), AC004805.1(1), LINC01140(1), GABRQ(1), AC010326.2(1), ERVV-1(1), BIVM-ERCC5(1), MTRNR2L11(1), MROH7-TTC4(1), RBAK-RBAKDN(1), CCL3L3(1), DHRS11(1), GIMAP1-GIMAP5(1)

5.4 Best C-index test in all runs

Best Elastic Net model (C-Index test)

[INFO] Coefs. list

[1] “ABCB4, AC008687.4, AC008758.6, ADM5, AJAP1, AL035460.1, AMH, ANAPC7, APCDD1L, AR, ASIC3, ATP8A1, BANF2, CCDC194, CCL22, CCL7, CCR10, CDCA7, CDRT15, CFAP45, CNTNAP1, COPS7B, CRP, CYP3A7, DEFB104A, DMRTC1, DNAAF6, DPAGT1, DRD5, EME1, ERFL, FAHD2A, FAM20A, FAM53B, FBXL5, FGF17, GPAT2, GPR78, HES7, HNRNPCL4, IL4, KBTBD11-OT1, KISS1, KLRC2, MAGEA5, MELTF, MKRN3, MPV17L, ONECUT2, OR8B4, OTX1, PABPC1L, PTX3, RHNO1, RNF183, SAGE1, SEC61A2, SERINC4, SIGLEC6, SLC18A3, SLC5A6, SLC7A5, SNF8, SNHG28, SORBS1, SPANXB1, SPATA18, SPRR2D, STRADA, USP17L8, VAMP3, Z84492.2, ZNF880”

Test set

Full set

Best Hub model (C-Index test)

[INFO] Coefs. list

[1] “AC099811.2, ACTA2, ACTC1, ACTG2, ADIPOQ, ALB, ANK3, AR, ATP2A1, CDC42, CDK2, CDK3, CDK6, CPLANE2, CSF3, DIRAS2, EFCAB11, EPHB2, FGFRL1, FOXP2, GGT2, GNAO1, HDAC1, HSPA8, IGF1R, IL4, IL6, INS, ISG15, JAK1, JUN, KAT2A, KDR, KMT5A, KRAS, MATK, MYC, NFKB1, NRAS, OAS2, PDE4D, PLK1, POTEI, POTEJ, PRDM10, PRKAG3, PRKCG, PTH, RABL2A, RAC3, RAP2A, RHOA, RHOB, RHOBTB3, RHOQ, RHOU, RHOV, RIPK4, RSKR, RXFP1, SFN, SGK1, SMARCA2, SRC, STAT3, TNF, TP53, UBB, UBC”

Test set

Full set

Best Orphan model (C-Index test)

[INFO] Coefs. list

[1] “AC008687.4, AC069503.2, AC138969.1, ADM5, ANHX, APCDD1L, AUP1, BORCS7, C16orf97, C1orf53, C20orf141, C2orf66, C4orf19, C4orf3, C9orf163, CCDC166, CCDC194, CCR10, CENPBD1, CFAP45, CKAP4, CLTRN, CPXCR1, CT45A8, DMRTC1, DSCR9, EMX2, ERICH5, ERV3-1, FAM72B, FAM72C, FBXL5, GOLGA6L9, GPR78, HES7, HS3ST3A1, IFT20, INAFM2, ITGA8, LIMCH1, LINC00313, LINC02870, MAGEA5, MMP24, NCOA4, ONECUT2, POLR3G, PTX3, RHNO1, RNF183, SAPCD1, SCGB1C2, SETSIP, SIGLEC6, SLC5A6, SMIM24, SNF8, SNHG28, SORBS1, SORBS2, SPANXB1, SPATA18, TEX29, TLCD1, TMEM200C, TMEM233, TMEM81, TPBGL, VRTN”

Test set

Full set

5.5 Best Log-rank test in all runs

Best Elastic net (Log-rank test)

[INFO] Coefs. list

[1] “AC138969.1, ADM5, AMOT, ANAPC7, AR, AUP1, B3GNTL1, CCL7, CDCA3, CLTRN, CNTNAP1, COL7A1, CRABP2, EIF4EBP2, EMX2, FBXL5, GPR173, HES7, IL4, IMPA2, ITGA8, LRFN1, METTL7A, MSH5-SAPCD1, NUF2, OTX1, PABPC1L, PIF1, PTX3, SAMM50, SEC61A2, SLC16A12, SLC2A6, SLC5A6, SLC7A5, SNF8, SORBS2, SPATA18, TRAIP, ZIC2, ZNF117”

Test set

Full set

Best Hub model (Log-rank test)

[INFO] Coefs. list

[1] “AC092143.1, ACTA2, ACTC1, ACTRT1, ALB, AR, BCL2, CAD, CALB2, CCL7, CDC42, CDK1, CDK16, CDK17, CDK2, CDK5, CDKN1A, CPLANE2, EPHB2, FGF2, FGFR3, FOSL1, GGT2, HDAC1, HSPA4L, HSPA8, IL4, IL6, ILK, INS, ISG15, JUN, KDR, KMT5A, KRAS, LRRK2, MATK, MGAM, MYC, NFKB1, PDE4D, PLK1, POTEI, POTEJ, PRDM10, PRKAG1, PRKAR2B, PTEN, PTH, RAC1, RAC3, REM2, RHOA, RHOBTB3, RHOU, RHOV, RIPK4, RSKR, SEC61A2, SRC, TNNT1, TOMM34, TP53, TTC32, TUBB2A, UBB, UBC, WDFY2, YARS1”

Test set

Full set

Best Orphan model (Log-rank test)

[INFO] Coefs. list

[1] “AC008687.4, AC069503.2, AC138969.1, ADM5, ANHX, APCDD1L, AUP1, BORCS7, C16orf97, C1orf53, C20orf141, C2orf66, C4orf19, C4orf3, C9orf163, CCDC166, CCDC194, CCR10, CENPBD1, CFAP45, CKAP4, CLTRN, CPXCR1, CT45A8, DMRTC1, DSCR9, EMX2, ERICH5, ERV3-1, FAM72B, FAM72C, FBXL5, GOLGA6L9, GPR78, HES7, HS3ST3A1, IFT20, INAFM2, ITGA8, LIMCH1, LINC00313, LINC02870, MAGEA5, MMP24, NCOA4, ONECUT2, POLR3G, PTX3, RHNO1, RNF183, SAPCD1, SCGB1C2, SETSIP, SIGLEC6, SLC5A6, SMIM24, SNF8, SNHG28, SORBS1, SORBS2, SPANXB1, SPATA18, TEX29, TLCD1, TMEM200C, TMEM233, TMEM81, TPBGL, VRTN”

Test set

Full set

NULL

6 Parameters for the report

## [INFO]          balanced.sets: TRUE
## [INFO]        calc.params.old: FALSE
## [INFO]           coding.genes: TRUE
## [INFO]     degree.correlation: pearson
## [INFO]          degree.cutoff:       0.000
## [INFO]            degree.type: string
## [INFO]      degree.unweighted: TRUE
## [INFO]      handle.duplicates: keep_first
## [INFO]                   log2: TRUE
## [INFO]                n.cores:      14.000
## [INFO]          normalization: center
## [INFO]                 ntimes:    5000.000
## [INFO]                project: kirc.data.2018.10.17
## [INFO]                   seed:    1985.000
## [INFO]                 subset: Inf
## [INFO]   subtract.surv.column: (I do not know how to display this)
## [INFO]            target.vars: list(alpha = 0.2, vars = 69), list(alpha = 0.1, vars = 41), list(alpha = 0.1, vars = 38)
## [INFO]                 tissue: primary.solid.tumor
## [INFO]                  train:       0.800